libgapmis: extending short-read alignments

BMC Bioinformatics

Table 5 Valid and correct alignments using needle.

Programme	Species	Length of queries [bp]	Gap occurrence frequency	Gap opening penalty	Gap extension penalty	Valid alignments	Correct alignments
needle	AT	100	2.4 × 10^-5	10.0	0.5	99,988	99,917
needle	AT	100	2.4 × 10^-5	15.0	0.5	99,992	99,911
needle	AT	100	2.4 × 10^-5	20.0	0.5	99,996	99,850
needle	AT	150	2.4 × 10^-5	10.0	0.5	99,991	99,919
needle	AT	150	2.4 × 10^-5	15.0	0.5	99,992	99,901
needle	AT	150	2.4 × 10^-5	20.0	0.5	99,996	99,834

The valid and correct alignments of 100, 000 pairs of simulated sequences with the gap occurrence frequency observed in Arabidopsis thaliana using needle. Each of the datasets consists of 100,000 pairs of sequences; the highest numbers of correct and valid alignments for each dataset are shown in bold.

ISSN: 1471-2105